• Caucasus ;
  • Darevskia ;
  • gene flow ;
  • lizards ;
  • microsatellites ;
  • mitochondrial DNA ;
  • multivariate morphometry ;
  • speciation ;
  • species boundaries

Given sufficient time and limited gene flow, evolutionary lineages tend to transform into separate species. Mechanisms preventing assimilation during repeated gene-flow events include divergent adaptations and the development of pre- or postzygotic isolation. We analysed the morphological and genetic boundaries of three species of the rock lizard clade Darevskiarudis’ (Darevskia rudis, Darevskia valentini, and Darevskia portschinskii) in relation to the environment, and tried to reconstruct evolutionary pathways underlying the observed separation among the species. We studied the geographic distribution of the scalation traits, microsatellite genotypes, and mitochondrial haplotypes. Our analyses showed consistent morphological and genetic patterns at the centre of the ranges for each species, but asymmetric distribution of alleles and scalation characters within the current contact zones among the species. The genetic and morphological diversification of the clade has been shaped during glacial isolation in an area of Southern Caucasus, away from the Black Sea Coast. The ancestral lineage of D. portschinskii separated from the common D. rudis–D. valentini lineage in the middle Pleistocene, and the two latter lineages separated in relatively recent geological time. Neither of the lineages attained complete lineage sorting; moreover, isolation and migration modelling have helped to detect recombinant gene flow from D. rudis to D. portschinskii (but not to D. valentini). This is most likely linked with climatically more similar suitable habitats between D. rudis and D. portschinskii than between D. valentini and the other two species. In itself, the isolation period was insufficient for the development of intrinsic isolation mechanisms in the system studied. Thus, differential landscape-dependent selection within the contact zones is likely to have triggered the rapid development of isolation mechanisms. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 109, 876–892.